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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A/HONG KONG/1/1968 (H3N2) INFLUENZA VIRUS HEMAGGLUTININ G225Q/L226A MUTANT IN COMPLEX WITH 3'-SLN
 
Authors :  N. C. Wu, I. A. Wilson
Date :  18 May 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  A,B,C,D,E,F  (1x)
Keywords :  Influenza A Virus, Hemagglutinin, Mutant, Receptor Binding, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. C. Wu, J. Xie, T. Zheng, C. M. Nycholat, G. Grande, J. C. Paulson, R. A. Lerner, I. A. Wilson
Diversity Of Functionally Permissive Sequences In The Receptor-Binding Site Of Influenza Hemagglutinin.
Cell Host Microbe V. 21 742 2017
PubMed-ID: 28618270  |  Reference-DOI: 10.1016/J.CHOM.2017.05.011

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1 CHAIN
    Chains: A, C, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HA
    Mutation: YES
    Organism Scientific: INFLUENZA A VIRUS (STRAIN A/HONG KONG/1/1968 H3N2)
    Organism Taxid: 506350
    Strain: A/HONG KONG/1/1968 H3N2
 
Molecule 2 - HEMAGGLUTININ HA2 CHAIN
    Chains: B, D, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (STRAIN A/HONG KONG/1/1968 H3N2)
    Organism Taxid: 506350
    Strain: A/HONG KONG/1/1968 H3N2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF
Biological Unit 4 (1x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA3Ligand/IonO-SIALIC ACID
Biological Unit 1 (5, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA1Ligand/IonO-SIALIC ACID
Biological Unit 2 (5, 10)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA1Ligand/IonO-SIALIC ACID
Biological Unit 3 (5, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA1Ligand/IonO-SIALIC ACID
Biological Unit 4 (5, 30)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2GAL3Ligand/IonBETA-D-GALACTOSE
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SIA3Ligand/IonO-SIALIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:37 , ASN A:38 , HOH A:513 , HOH A:555binding site for Mono-Saccharide NAG A 407 bound to ASN A 38
02AC2SOFTWAREASN A:165 , THR A:167 , HOH A:502 , HOH A:551 , HOH A:557 , HOH A:580 , HOH A:603 , SER C:219 , PRO C:221 , TRP C:222 , NAG C:410 , THR E:83 , GLU E:119binding site for Poly-Saccharide residues NAG A 401 through MAN A 404 bound to ASN A 165
03AC3SOFTWARESER A:45 , ASN A:285 , VAL A:297 , ASN A:298 , HOH A:595 , GLU B:69binding site for Poly-Saccharide residues NAG A 405 through NAG A 406 bound to ASN A 285
04AC4SOFTWAREASN C:165 , THR C:167 , ARG C:207 , HOH C:503 , HOH C:504 , HOH C:525 , HOH C:647 , SER E:219 , PRO E:221 , TRP E:222 , NAG E:511binding site for Poly-Saccharide residues NAG C 401 through MAN C 405 bound to ASN C 165
05AC5SOFTWARESER C:45 , ASN C:285 , VAL C:297 , ASN C:298 , HOH C:598 , HOH C:648 , GLU D:69binding site for Poly-Saccharide residues NAG C 406 through NAG C 407 bound to ASN C 285
06AC6SOFTWAREASN E:38 , ALA E:39 , THR E:40 , HOH E:605 , HOH E:671binding site for Mono-Saccharide NAG E 501 bound to ASN E 38
07AC7SOFTWAREGLN E:80 , ASN E:81 , GLU E:119 , PHE E:120 , HOH E:609 , HOH E:661binding site for Mono-Saccharide NAG E 508 bound to ASN E 81
08AC8SOFTWARESER A:219 , PRO A:221 , TRP A:222 , ASN E:165 , THR E:167 , HOH E:637 , HOH E:666binding site for Poly-Saccharide residues NAG E 502 through MAN E 505 bound to ASN E 165
09AC9SOFTWARESER E:45 , ASN E:285 , VAL E:297 , HOH E:667 , HOH E:676 , GLU F:69binding site for Poly-Saccharide residues NAG E 506 through NAG E 507 bound to ASN E 285
10AD1SOFTWARETYR A:98 , GLY A:134 , GLY A:135 , SER A:136 , ASN A:137 , TRP A:153 , GLU A:190 , LEU A:194 , GLN A:225 , SER A:228binding site for Poly-Saccharide residues SIA A 408 through GAL A 409
11AD2SOFTWAREMAN A:404 , TYR C:98 , GLY C:134 , GLY C:135 , SER C:136 , ASN C:137 , TRP C:153 , GLU C:190 , LEU C:194 , GLN C:225 , SER C:228 , HOH C:646binding site for Poly-Saccharide residues SIA C 408 through NAG C 410
12AD3SOFTWAREMAN A:404 , ASP C:63 , CYS C:64 , THR C:65 , ASP C:68 , PHE C:94 , ASP C:172 , GLU C:190 , THR C:203 , SER C:205 , GLN C:225 , VAL C:244 , TYR C:257 , NAG C:402 , SIA C:408 , HOH C:545 , HOH C:647 , TYR E:98 , GLY E:134 , GLY E:135 , SER E:136 , ASN E:137 , GLU E:190 , LEU E:194 , SER E:219 , GLN E:225 , SER E:228binding site for Poly-Saccharide residues SIA E 509 through NAG E 511

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:14 -B:137
2A:52 -A:277
3A:64 -A:76
4A:97 -A:139
5A:281 -A:305
6B:144 -B:148
7C:14 -D:137
8C:52 -C:277
9C:64 -C:76
10C:97 -C:139
11C:281 -C:305
12D:144 -D:148
13E:14 -F:137
14E:52 -E:277
15E:64 -E:76
16E:97 -E:139
17E:281 -E:305
18F:144 -F:148

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn A:54 -Pro A:55
2Asn C:54 -Pro C:55
3Asn E:54 -Pro E:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VTY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VTY)

(-) Exons   (0, 0)

(no "Exon" information available for 5VTY)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......eeeee.eeeeee..eee....eeeeee.......eeeeee......eeeeeeeee..hhhhhhhhhh....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee....eeeee..eee..eee.....ee.......ee..ee......eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vty A  10 GATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRQASSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPE 325
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319      


Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vty B   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......eeeee.eeeeee..eee....eeeeee.......eeeeee......eeeeeeeee..hhhhhhhhhh....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee....eeeee..eee..eee.....ee.......ee..ee......eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vty C   9 PGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRQASSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPE 325
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       


Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vty D   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain E from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eee.......eee..eee.ee......eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......eeeee.eeeeee..eee....eeeeee.......eeeeee......eeeeeeeee..hhhhhhhhhh....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee....eeeee..eee..eee.....ee.......ee..ee......eee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vty E   9 PGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRQASSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTR 329
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328 


Chain F from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhh....ee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vty F   1 GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5VTY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VTY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VTY)

(-) Gene Ontology  (17, 17)

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  5vty
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  HEMA_I68A4 | Q91MA7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HEMA_I68A4 | Q91MA7: 3sdy 3ztj 4fnk 4fp8 4fqr 4fqy 4nm8 4ubd 4we4 4zcj 5k9k 5k9q 5kan 5kuy 5t6n 5thf 5umn 5vtq 5vtr 5vtu 5vtv 5vtw 5vtx 5vtz 5vu4

(-) Related Entries Specified in the PDB File

5vtq 5vtr 5vtu 5vtv 5vtw 5vtx 5vtz 5vu4